Starting phenix.real_space_refine on Sun Aug 24 08:19:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fj5_29215/08_2025/8fj5_29215.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fj5_29215/08_2025/8fj5_29215.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fj5_29215/08_2025/8fj5_29215.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fj5_29215/08_2025/8fj5_29215.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fj5_29215/08_2025/8fj5_29215.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fj5_29215/08_2025/8fj5_29215.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.077 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 11740 2.51 5 N 2980 2.21 5 O 4240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18980 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 949 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 3, 'TRANS': 129} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T Time building chain proxies: 1.38, per 1000 atoms: 0.07 Number of scatterers: 18980 At special positions: 0 Unit cell: (97.44, 98.56, 202.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 4240 8.00 N 2980 7.00 C 11740 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 887.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4720 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 60 sheets defined 26.4% alpha, 45.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 13 through 42 removed outlier: 3.610A pdb=" N ILE A 28 " --> pdb=" O ALA A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP A 96 " --> pdb=" O TRP A 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP B 96 " --> pdb=" O TRP B 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP C 96 " --> pdb=" O TRP C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE D 28 " --> pdb=" O ALA D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP D 96 " --> pdb=" O TRP D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE E 28 " --> pdb=" O ALA E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP E 96 " --> pdb=" O TRP E 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE F 28 " --> pdb=" O ALA F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP F 96 " --> pdb=" O TRP F 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE G 28 " --> pdb=" O ALA G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP G 96 " --> pdb=" O TRP G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE H 28 " --> pdb=" O ALA H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP H 96 " --> pdb=" O TRP H 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE I 28 " --> pdb=" O ALA I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP I 96 " --> pdb=" O TRP I 92 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE J 28 " --> pdb=" O ALA J 24 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP J 96 " --> pdb=" O TRP J 92 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE K 28 " --> pdb=" O ALA K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP K 96 " --> pdb=" O TRP K 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE L 28 " --> pdb=" O ALA L 24 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP L 96 " --> pdb=" O TRP L 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE M 28 " --> pdb=" O ALA M 24 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 96 removed outlier: 3.747A pdb=" N ASP M 96 " --> pdb=" O TRP M 92 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE N 28 " --> pdb=" O ALA N 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP N 96 " --> pdb=" O TRP N 92 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP O 96 " --> pdb=" O TRP O 92 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE P 28 " --> pdb=" O ALA P 24 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP P 96 " --> pdb=" O TRP P 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP Q 96 " --> pdb=" O TRP Q 92 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE R 28 " --> pdb=" O ALA R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP R 96 " --> pdb=" O TRP R 92 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE S 28 " --> pdb=" O ALA S 24 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP S 96 " --> pdb=" O TRP S 92 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 42 removed outlier: 3.610A pdb=" N ILE T 28 " --> pdb=" O ALA T 24 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 96 removed outlier: 3.748A pdb=" N ASP T 96 " --> pdb=" O TRP T 92 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 58 removed outlier: 6.759A pdb=" N SER A 52 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 63 " --> pdb=" O THR A 58 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 58 removed outlier: 6.759A pdb=" N SER A 52 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN A 63 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR A 65 " --> pdb=" O TRP I 141 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP I 141 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR A 67 " --> pdb=" O GLN I 139 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN I 139 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU A 69 " --> pdb=" O THR I 137 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR I 137 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL I 125 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER I 140 " --> pdb=" O VAL I 123 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL I 123 " --> pdb=" O SER I 140 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA4, first strand: chain 'A' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL A 123 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER A 140 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 125 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 137 " --> pdb=" O GLU N 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU N 69 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN A 139 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR N 67 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP A 141 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR N 65 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN N 63 " --> pdb=" O THR N 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER N 52 " --> pdb=" O GLU N 69 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL A 123 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER A 140 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL A 125 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR A 137 " --> pdb=" O GLU N 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU N 69 " --> pdb=" O THR A 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN A 139 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR N 67 " --> pdb=" O GLN A 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP A 141 " --> pdb=" O THR N 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR N 65 " --> pdb=" O TRP A 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 51 through 58 removed outlier: 6.759A pdb=" N SER B 52 " --> pdb=" O GLU B 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 63 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 74 through 75 Processing sheet with id=AA8, first strand: chain 'B' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL B 123 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 140 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 125 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 137 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU E 69 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN B 139 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR E 67 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP B 141 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR E 65 " --> pdb=" O TRP B 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN E 63 " --> pdb=" O THR E 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER E 52 " --> pdb=" O GLU E 69 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL B 123 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER B 140 " --> pdb=" O VAL B 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL B 125 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 137 " --> pdb=" O GLU E 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU E 69 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN B 139 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR E 67 " --> pdb=" O GLN B 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP B 141 " --> pdb=" O THR E 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR E 65 " --> pdb=" O TRP B 141 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 51 through 58 removed outlier: 6.758A pdb=" N SER C 52 " --> pdb=" O GLU C 69 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN C 63 " --> pdb=" O THR C 58 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 74 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.461A pdb=" N VAL C 123 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER C 140 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 125 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 137 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU F 69 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN C 139 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR F 67 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP C 141 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR F 65 " --> pdb=" O TRP C 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN F 63 " --> pdb=" O THR F 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER F 52 " --> pdb=" O GLU F 69 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.461A pdb=" N VAL C 123 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER C 140 " --> pdb=" O VAL C 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 125 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR C 137 " --> pdb=" O GLU F 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU F 69 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN C 139 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR F 67 " --> pdb=" O GLN C 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP C 141 " --> pdb=" O THR F 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR F 65 " --> pdb=" O TRP C 141 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 51 through 58 removed outlier: 6.760A pdb=" N SER D 52 " --> pdb=" O GLU D 69 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN D 63 " --> pdb=" O THR D 58 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 74 through 75 Processing sheet with id=AB7, first strand: chain 'D' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL D 123 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER D 140 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 125 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 137 " --> pdb=" O GLU G 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU G 69 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN D 139 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR G 67 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP D 141 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR G 65 " --> pdb=" O TRP D 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN G 63 " --> pdb=" O THR G 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER G 52 " --> pdb=" O GLU G 69 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL D 123 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER D 140 " --> pdb=" O VAL D 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL D 125 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR D 137 " --> pdb=" O GLU G 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU G 69 " --> pdb=" O THR D 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN D 139 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR G 67 " --> pdb=" O GLN D 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP D 141 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR G 65 " --> pdb=" O TRP D 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 74 through 75 Processing sheet with id=AC1, first strand: chain 'E' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL E 123 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER E 140 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL E 125 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 137 " --> pdb=" O GLU H 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU H 69 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN E 139 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR H 67 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP E 141 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR H 65 " --> pdb=" O TRP E 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN H 63 " --> pdb=" O THR H 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER H 52 " --> pdb=" O GLU H 69 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL E 123 " --> pdb=" O SER E 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER E 140 " --> pdb=" O VAL E 123 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL E 125 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 137 " --> pdb=" O GLU H 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU H 69 " --> pdb=" O THR E 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN E 139 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR H 67 " --> pdb=" O GLN E 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP E 141 " --> pdb=" O THR H 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR H 65 " --> pdb=" O TRP E 141 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 74 through 75 Processing sheet with id=AC4, first strand: chain 'F' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL F 123 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER F 140 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 125 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 137 " --> pdb=" O GLU I 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU I 69 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN F 139 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR I 67 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP F 141 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR I 65 " --> pdb=" O TRP F 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN I 63 " --> pdb=" O THR I 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER I 52 " --> pdb=" O GLU I 69 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL F 123 " --> pdb=" O SER F 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER F 140 " --> pdb=" O VAL F 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL F 125 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 137 " --> pdb=" O GLU I 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU I 69 " --> pdb=" O THR F 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN F 139 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR I 67 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP F 141 " --> pdb=" O THR I 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR I 65 " --> pdb=" O TRP F 141 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 74 through 75 Processing sheet with id=AC7, first strand: chain 'G' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL G 123 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER G 140 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 125 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 137 " --> pdb=" O GLU J 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU J 69 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN G 139 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR J 67 " --> pdb=" O GLN G 139 " (cutoff:3.500A) removed outlier: 15.522A pdb=" N TRP G 141 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR J 65 " --> pdb=" O TRP G 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN J 63 " --> pdb=" O THR J 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER J 52 " --> pdb=" O GLU J 69 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL G 123 " --> pdb=" O SER G 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER G 140 " --> pdb=" O VAL G 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL G 125 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR G 137 " --> pdb=" O GLU J 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU J 69 " --> pdb=" O THR G 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN G 139 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR J 67 " --> pdb=" O GLN G 139 " (cutoff:3.500A) removed outlier: 15.522A pdb=" N TRP G 141 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR J 65 " --> pdb=" O TRP G 141 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'H' and resid 74 through 75 Processing sheet with id=AD1, first strand: chain 'H' and resid 79 through 82 removed outlier: 6.461A pdb=" N VAL H 123 " --> pdb=" O SER H 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER H 140 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 125 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR H 137 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU K 69 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN H 139 " --> pdb=" O THR K 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR K 67 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP H 141 " --> pdb=" O THR K 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR K 65 " --> pdb=" O TRP H 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN K 63 " --> pdb=" O THR K 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER K 52 " --> pdb=" O GLU K 69 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 79 through 82 removed outlier: 6.461A pdb=" N VAL H 123 " --> pdb=" O SER H 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER H 140 " --> pdb=" O VAL H 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL H 125 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR H 137 " --> pdb=" O GLU K 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU K 69 " --> pdb=" O THR H 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN H 139 " --> pdb=" O THR K 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR K 67 " --> pdb=" O GLN H 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP H 141 " --> pdb=" O THR K 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR K 65 " --> pdb=" O TRP H 141 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 74 through 75 Processing sheet with id=AD4, first strand: chain 'J' and resid 74 through 75 Processing sheet with id=AD5, first strand: chain 'J' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL J 123 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER J 140 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL J 125 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR J 137 " --> pdb=" O GLU L 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU L 69 " --> pdb=" O THR J 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN J 139 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR L 67 " --> pdb=" O GLN J 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP J 141 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR L 65 " --> pdb=" O TRP J 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN L 63 " --> pdb=" O THR L 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER L 52 " --> pdb=" O GLU L 69 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL J 123 " --> pdb=" O SER J 140 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER J 140 " --> pdb=" O VAL J 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL J 125 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR J 137 " --> pdb=" O GLU L 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU L 69 " --> pdb=" O THR J 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN J 139 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR L 67 " --> pdb=" O GLN J 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP J 141 " --> pdb=" O THR L 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR L 65 " --> pdb=" O TRP J 141 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 74 through 75 Processing sheet with id=AD8, first strand: chain 'K' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL K 123 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER K 140 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL K 125 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR K 137 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU M 69 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN K 139 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR M 67 " --> pdb=" O GLN K 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP K 141 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR M 65 " --> pdb=" O TRP K 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN M 63 " --> pdb=" O THR M 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER M 52 " --> pdb=" O GLU M 69 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL K 123 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER K 140 " --> pdb=" O VAL K 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL K 125 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR K 137 " --> pdb=" O GLU M 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU M 69 " --> pdb=" O THR K 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN K 139 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR M 67 " --> pdb=" O GLN K 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP K 141 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 16.129A pdb=" N THR M 65 " --> pdb=" O TRP K 141 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 74 through 75 Processing sheet with id=AE2, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL L 123 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER L 140 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL L 125 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 137 " --> pdb=" O GLU O 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU O 69 " --> pdb=" O THR L 137 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N GLN L 139 " --> pdb=" O THR O 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR O 67 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP L 141 " --> pdb=" O THR O 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR O 65 " --> pdb=" O TRP L 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN O 63 " --> pdb=" O THR O 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER O 52 " --> pdb=" O GLU O 69 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'L' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL L 123 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER L 140 " --> pdb=" O VAL L 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL L 125 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR L 137 " --> pdb=" O GLU O 69 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLU O 69 " --> pdb=" O THR L 137 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N GLN L 139 " --> pdb=" O THR O 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR O 67 " --> pdb=" O GLN L 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP L 141 " --> pdb=" O THR O 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR O 65 " --> pdb=" O TRP L 141 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 74 through 75 Processing sheet with id=AE5, first strand: chain 'M' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL M 123 " --> pdb=" O SER M 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER M 140 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL M 125 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR M 137 " --> pdb=" O GLU P 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU P 69 " --> pdb=" O THR M 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN M 139 " --> pdb=" O THR P 67 " (cutoff:3.500A) removed outlier: 14.234A pdb=" N THR P 67 " --> pdb=" O GLN M 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP M 141 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR P 65 " --> pdb=" O TRP M 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN P 63 " --> pdb=" O THR P 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER P 52 " --> pdb=" O GLU P 69 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL M 123 " --> pdb=" O SER M 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER M 140 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL M 125 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR M 137 " --> pdb=" O GLU P 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU P 69 " --> pdb=" O THR M 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN M 139 " --> pdb=" O THR P 67 " (cutoff:3.500A) removed outlier: 14.234A pdb=" N THR P 67 " --> pdb=" O GLN M 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP M 141 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR P 65 " --> pdb=" O TRP M 141 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'N' and resid 74 through 75 Processing sheet with id=AE8, first strand: chain 'N' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL N 123 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER N 140 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL N 125 " --> pdb=" O LEU N 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR N 137 " --> pdb=" O GLU Q 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU Q 69 " --> pdb=" O THR N 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN N 139 " --> pdb=" O THR Q 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR Q 67 " --> pdb=" O GLN N 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP N 141 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR Q 65 " --> pdb=" O TRP N 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN Q 63 " --> pdb=" O THR Q 58 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER Q 52 " --> pdb=" O GLU Q 69 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL N 123 " --> pdb=" O SER N 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER N 140 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL N 125 " --> pdb=" O LEU N 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR N 137 " --> pdb=" O GLU Q 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU Q 69 " --> pdb=" O THR N 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN N 139 " --> pdb=" O THR Q 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR Q 67 " --> pdb=" O GLN N 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP N 141 " --> pdb=" O THR Q 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR Q 65 " --> pdb=" O TRP N 141 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'O' and resid 74 through 75 Processing sheet with id=AF2, first strand: chain 'O' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL O 123 " --> pdb=" O SER O 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER O 140 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL O 125 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR O 137 " --> pdb=" O GLU R 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU R 69 " --> pdb=" O THR O 137 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N GLN O 139 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR R 67 " --> pdb=" O GLN O 139 " (cutoff:3.500A) removed outlier: 15.520A pdb=" N TRP O 141 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR R 65 " --> pdb=" O TRP O 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN R 63 " --> pdb=" O THR R 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER R 52 " --> pdb=" O GLU R 69 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'O' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL O 123 " --> pdb=" O SER O 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER O 140 " --> pdb=" O VAL O 123 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL O 125 " --> pdb=" O LEU O 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR O 137 " --> pdb=" O GLU R 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU R 69 " --> pdb=" O THR O 137 " (cutoff:3.500A) removed outlier: 13.550A pdb=" N GLN O 139 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR R 67 " --> pdb=" O GLN O 139 " (cutoff:3.500A) removed outlier: 15.520A pdb=" N TRP O 141 " --> pdb=" O THR R 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR R 65 " --> pdb=" O TRP O 141 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 74 through 75 Processing sheet with id=AF5, first strand: chain 'P' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL P 123 " --> pdb=" O SER P 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER P 140 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL P 125 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR P 137 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU S 69 " --> pdb=" O THR P 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN P 139 " --> pdb=" O THR S 67 " (cutoff:3.500A) removed outlier: 14.234A pdb=" N THR S 67 " --> pdb=" O GLN P 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP P 141 " --> pdb=" O THR S 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR S 65 " --> pdb=" O TRP P 141 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN S 63 " --> pdb=" O THR S 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER S 52 " --> pdb=" O GLU S 69 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL P 123 " --> pdb=" O SER P 140 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N SER P 140 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL P 125 " --> pdb=" O LEU P 138 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR P 137 " --> pdb=" O GLU S 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU S 69 " --> pdb=" O THR P 137 " (cutoff:3.500A) removed outlier: 13.549A pdb=" N GLN P 139 " --> pdb=" O THR S 67 " (cutoff:3.500A) removed outlier: 14.234A pdb=" N THR S 67 " --> pdb=" O GLN P 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP P 141 " --> pdb=" O THR S 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR S 65 " --> pdb=" O TRP P 141 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 74 through 75 Processing sheet with id=AF8, first strand: chain 'Q' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL Q 123 " --> pdb=" O SER Q 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER Q 140 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL Q 125 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR Q 137 " --> pdb=" O GLU T 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU T 69 " --> pdb=" O THR Q 137 " (cutoff:3.500A) removed outlier: 13.548A pdb=" N GLN Q 139 " --> pdb=" O THR T 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR T 67 " --> pdb=" O GLN Q 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP Q 141 " --> pdb=" O THR T 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR T 65 " --> pdb=" O TRP Q 141 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN T 63 " --> pdb=" O THR T 58 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N SER T 52 " --> pdb=" O GLU T 69 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'Q' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL Q 123 " --> pdb=" O SER Q 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER Q 140 " --> pdb=" O VAL Q 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL Q 125 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR Q 137 " --> pdb=" O GLU T 69 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLU T 69 " --> pdb=" O THR Q 137 " (cutoff:3.500A) removed outlier: 13.548A pdb=" N GLN Q 139 " --> pdb=" O THR T 67 " (cutoff:3.500A) removed outlier: 14.233A pdb=" N THR T 67 " --> pdb=" O GLN Q 139 " (cutoff:3.500A) removed outlier: 15.521A pdb=" N TRP Q 141 " --> pdb=" O THR T 65 " (cutoff:3.500A) removed outlier: 16.130A pdb=" N THR T 65 " --> pdb=" O TRP Q 141 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'R' and resid 74 through 75 Processing sheet with id=AG2, first strand: chain 'R' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL R 123 " --> pdb=" O SER R 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER R 140 " --> pdb=" O VAL R 123 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N VAL R 125 " --> pdb=" O LEU R 138 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 74 through 75 Processing sheet with id=AG4, first strand: chain 'S' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL S 123 " --> pdb=" O SER S 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER S 140 " --> pdb=" O VAL S 123 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL S 125 " --> pdb=" O LEU S 138 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'T' and resid 74 through 75 Processing sheet with id=AG6, first strand: chain 'T' and resid 79 through 82 removed outlier: 6.462A pdb=" N VAL T 123 " --> pdb=" O SER T 140 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER T 140 " --> pdb=" O VAL T 123 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL T 125 " --> pdb=" O LEU T 138 " (cutoff:3.500A) 1065 hydrogen bonds defined for protein. 3135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.69 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6260 1.34 - 1.46: 3763 1.46 - 1.57: 9217 1.57 - 1.69: 0 1.69 - 1.80: 40 Bond restraints: 19280 Sorted by residual: bond pdb=" CG1 ILE K 33 " pdb=" CD1 ILE K 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.28e+00 bond pdb=" CG1 ILE M 33 " pdb=" CD1 ILE M 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.27e+00 bond pdb=" CG1 ILE H 33 " pdb=" CD1 ILE H 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.26e+00 bond pdb=" CG1 ILE E 33 " pdb=" CD1 ILE E 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.25e+00 bond pdb=" CG1 ILE P 33 " pdb=" CD1 ILE P 33 " ideal model delta sigma weight residual 1.513 1.454 0.059 3.90e-02 6.57e+02 2.25e+00 ... (remaining 19275 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.08: 24609 1.08 - 2.15: 1492 2.15 - 3.23: 219 3.23 - 4.31: 59 4.31 - 5.38: 41 Bond angle restraints: 26420 Sorted by residual: angle pdb=" N GLU M 46 " pdb=" CA GLU M 46 " pdb=" C GLU M 46 " ideal model delta sigma weight residual 110.91 114.58 -3.67 1.17e+00 7.31e-01 9.85e+00 angle pdb=" N GLU R 46 " pdb=" CA GLU R 46 " pdb=" C GLU R 46 " ideal model delta sigma weight residual 110.91 114.57 -3.66 1.17e+00 7.31e-01 9.78e+00 angle pdb=" N GLU I 46 " pdb=" CA GLU I 46 " pdb=" C GLU I 46 " ideal model delta sigma weight residual 110.91 114.56 -3.65 1.17e+00 7.31e-01 9.74e+00 angle pdb=" N GLU Q 46 " pdb=" CA GLU Q 46 " pdb=" C GLU Q 46 " ideal model delta sigma weight residual 110.91 114.56 -3.65 1.17e+00 7.31e-01 9.72e+00 angle pdb=" N GLU H 46 " pdb=" CA GLU H 46 " pdb=" C GLU H 46 " ideal model delta sigma weight residual 110.91 114.56 -3.65 1.17e+00 7.31e-01 9.71e+00 ... (remaining 26415 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.68: 9840 12.68 - 25.37: 780 25.37 - 38.05: 280 38.05 - 50.73: 100 50.73 - 63.42: 20 Dihedral angle restraints: 11020 sinusoidal: 3620 harmonic: 7400 Sorted by residual: dihedral pdb=" CA GLY G 97 " pdb=" C GLY G 97 " pdb=" N SER G 98 " pdb=" CA SER G 98 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY F 97 " pdb=" C GLY F 97 " pdb=" N SER F 98 " pdb=" CA SER F 98 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA GLY D 97 " pdb=" C GLY D 97 " pdb=" N SER D 98 " pdb=" CA SER D 98 " ideal model delta harmonic sigma weight residual -180.00 -162.63 -17.37 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 11017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1739 0.028 - 0.056: 1006 0.056 - 0.084: 349 0.084 - 0.112: 126 0.112 - 0.140: 100 Chirality restraints: 3320 Sorted by residual: chirality pdb=" CA SER C 14 " pdb=" N SER C 14 " pdb=" C SER C 14 " pdb=" CB SER C 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA SER E 14 " pdb=" N SER E 14 " pdb=" C SER E 14 " pdb=" CB SER E 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.84e-01 chirality pdb=" CA SER I 14 " pdb=" N SER I 14 " pdb=" C SER I 14 " pdb=" CB SER I 14 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 3317 not shown) Planarity restraints: 3360 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE C 33 " 0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ILE C 33 " -0.023 2.00e-02 2.50e+03 pdb=" O ILE C 33 " 0.009 2.00e-02 2.50e+03 pdb=" N GLY C 34 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 33 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ILE R 33 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE R 33 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY R 34 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE O 33 " -0.007 2.00e-02 2.50e+03 1.32e-02 1.73e+00 pdb=" C ILE O 33 " 0.023 2.00e-02 2.50e+03 pdb=" O ILE O 33 " -0.009 2.00e-02 2.50e+03 pdb=" N GLY O 34 " -0.008 2.00e-02 2.50e+03 ... (remaining 3357 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 7417 2.89 - 3.39: 16953 3.39 - 3.90: 30518 3.90 - 4.40: 35604 4.40 - 4.90: 60971 Nonbonded interactions: 151463 Sorted by model distance: nonbonded pdb=" O VAL R 44 " pdb=" OG SER R 45 " model vdw 2.391 3.040 nonbonded pdb=" O VAL F 44 " pdb=" OG SER F 45 " model vdw 2.392 3.040 nonbonded pdb=" O VAL S 44 " pdb=" OG SER S 45 " model vdw 2.392 3.040 nonbonded pdb=" O VAL I 44 " pdb=" OG SER I 45 " model vdw 2.392 3.040 nonbonded pdb=" O VAL H 44 " pdb=" OG SER H 45 " model vdw 2.392 3.040 ... (remaining 151458 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.330 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 19280 Z= 0.187 Angle : 0.621 5.383 26420 Z= 0.369 Chirality : 0.044 0.140 3320 Planarity : 0.003 0.027 3360 Dihedral : 11.786 63.417 6300 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.51 (0.16), residues: 2620 helix: 3.65 (0.15), residues: 600 sheet: 1.16 (0.17), residues: 1000 loop : -0.86 (0.17), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG N 124 TYR 0.005 0.001 TYR D 143 PHE 0.008 0.001 PHE R 55 TRP 0.010 0.002 TRP D 92 HIS 0.001 0.000 HIS T 68 Details of bonding type rmsd covalent geometry : bond 0.00424 (19280) covalent geometry : angle 0.62093 (26420) hydrogen bonds : bond 0.17440 ( 915) hydrogen bonds : angle 5.25526 ( 3135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 382 time to evaluate : 0.744 Fit side-chains REVERT: C 50 GLN cc_start: 0.8543 (mt0) cc_final: 0.8309 (mt0) REVERT: C 90 LYS cc_start: 0.8808 (mtmt) cc_final: 0.8543 (mtmt) REVERT: D 40 LEU cc_start: 0.8692 (tt) cc_final: 0.8440 (tp) REVERT: D 116 SER cc_start: 0.8724 (p) cc_final: 0.8374 (m) REVERT: D 130 ASP cc_start: 0.7967 (m-30) cc_final: 0.7714 (m-30) REVERT: F 33 ILE cc_start: 0.8440 (mt) cc_final: 0.8203 (tp) REVERT: F 40 LEU cc_start: 0.8378 (tt) cc_final: 0.8136 (tp) REVERT: F 59 ASN cc_start: 0.8877 (t0) cc_final: 0.7943 (t0) REVERT: G 59 ASN cc_start: 0.8913 (t0) cc_final: 0.8376 (t0) REVERT: G 130 ASP cc_start: 0.7888 (m-30) cc_final: 0.7682 (m-30) REVERT: H 22 MET cc_start: 0.8432 (mmp) cc_final: 0.8041 (mmp) REVERT: H 33 ILE cc_start: 0.8602 (mt) cc_final: 0.8382 (tp) REVERT: H 59 ASN cc_start: 0.8898 (t0) cc_final: 0.8650 (t0) REVERT: H 88 ASP cc_start: 0.8051 (t70) cc_final: 0.7737 (t70) REVERT: I 25 ILE cc_start: 0.8651 (mt) cc_final: 0.8386 (mm) REVERT: I 75 ASP cc_start: 0.8109 (t0) cc_final: 0.7782 (t0) REVERT: J 56 ASP cc_start: 0.8224 (t70) cc_final: 0.7961 (t70) REVERT: J 94 ASP cc_start: 0.7851 (m-30) cc_final: 0.7508 (m-30) REVERT: K 121 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8372 (mt-10) REVERT: M 94 ASP cc_start: 0.8019 (m-30) cc_final: 0.7628 (m-30) REVERT: M 130 ASP cc_start: 0.7970 (m-30) cc_final: 0.7671 (m-30) REVERT: N 130 ASP cc_start: 0.8159 (m-30) cc_final: 0.7887 (m-30) REVERT: P 50 GLN cc_start: 0.8631 (mt0) cc_final: 0.8328 (mt0) REVERT: P 56 ASP cc_start: 0.8055 (t70) cc_final: 0.7826 (t70) REVERT: Q 50 GLN cc_start: 0.8578 (mt0) cc_final: 0.8330 (mt0) REVERT: Q 56 ASP cc_start: 0.8022 (t70) cc_final: 0.7779 (t70) REVERT: Q 59 ASN cc_start: 0.8924 (t0) cc_final: 0.8512 (t0) REVERT: S 54 ASP cc_start: 0.8114 (t70) cc_final: 0.7873 (t0) REVERT: S 130 ASP cc_start: 0.7737 (m-30) cc_final: 0.7434 (m-30) REVERT: T 94 ASP cc_start: 0.8128 (m-30) cc_final: 0.7792 (m-30) REVERT: T 121 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8288 (mt-10) outliers start: 0 outliers final: 0 residues processed: 382 average time/residue: 0.4154 time to fit residues: 185.8428 Evaluate side-chains 307 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 307 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.0370 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN E 50 GLN G 50 GLN I 50 GLN J 50 GLN L 50 GLN N 50 GLN P 50 GLN S 50 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.108905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.090384 restraints weight = 22540.082| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.54 r_work: 0.2724 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2594 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19280 Z= 0.133 Angle : 0.500 7.741 26420 Z= 0.280 Chirality : 0.043 0.148 3320 Planarity : 0.003 0.024 3360 Dihedral : 4.883 16.860 2700 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.92 % Allowed : 4.22 % Favored : 94.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.16), residues: 2620 helix: 3.07 (0.18), residues: 700 sheet: 1.66 (0.17), residues: 960 loop : -1.19 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 124 TYR 0.008 0.001 TYR M 143 PHE 0.010 0.001 PHE K 55 TRP 0.011 0.001 TRP F 141 HIS 0.005 0.002 HIS Q 68 Details of bonding type rmsd covalent geometry : bond 0.00296 (19280) covalent geometry : angle 0.49979 (26420) hydrogen bonds : bond 0.06459 ( 915) hydrogen bonds : angle 3.67596 ( 3135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 302 time to evaluate : 0.674 Fit side-chains REVERT: B 50 GLN cc_start: 0.8946 (mt0) cc_final: 0.8633 (mt0) REVERT: D 116 SER cc_start: 0.8724 (p) cc_final: 0.8310 (m) REVERT: E 40 LEU cc_start: 0.8362 (tp) cc_final: 0.8156 (tt) REVERT: E 94 ASP cc_start: 0.7794 (m-30) cc_final: 0.7533 (m-30) REVERT: F 33 ILE cc_start: 0.8405 (mt) cc_final: 0.8114 (tp) REVERT: F 56 ASP cc_start: 0.8655 (t0) cc_final: 0.8377 (t70) REVERT: F 59 ASN cc_start: 0.8992 (t0) cc_final: 0.8718 (t0) REVERT: G 59 ASN cc_start: 0.8995 (t0) cc_final: 0.8640 (t0) REVERT: H 101 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: I 25 ILE cc_start: 0.8824 (mt) cc_final: 0.8571 (mm) REVERT: J 56 ASP cc_start: 0.8795 (t70) cc_final: 0.8575 (t70) REVERT: K 121 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8506 (mt-10) REVERT: M 130 ASP cc_start: 0.8242 (m-30) cc_final: 0.8023 (m-30) REVERT: P 59 ASN cc_start: 0.9036 (t0) cc_final: 0.8571 (t0) REVERT: Q 50 GLN cc_start: 0.8701 (mt0) cc_final: 0.8473 (mt0) REVERT: Q 59 ASN cc_start: 0.9080 (t0) cc_final: 0.8717 (t0) REVERT: Q 101 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7920 (tt0) REVERT: S 101 GLU cc_start: 0.8025 (mm-30) cc_final: 0.7579 (tp30) REVERT: S 130 ASP cc_start: 0.8337 (m-30) cc_final: 0.8027 (m-30) REVERT: T 94 ASP cc_start: 0.8093 (m-30) cc_final: 0.7529 (m-30) REVERT: T 121 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8437 (mt-10) outliers start: 20 outliers final: 11 residues processed: 309 average time/residue: 0.4848 time to fit residues: 172.9425 Evaluate side-chains 283 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 270 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 101 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 51 optimal weight: 4.9990 chunk 214 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 127 optimal weight: 0.0570 chunk 118 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 157 optimal weight: 0.7980 chunk 210 optimal weight: 0.8980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN F 50 GLN H 50 GLN L 50 GLN N 50 GLN P 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.112188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.094010 restraints weight = 22490.728| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 1.51 r_work: 0.2784 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 19280 Z= 0.105 Angle : 0.451 6.039 26420 Z= 0.250 Chirality : 0.042 0.141 3320 Planarity : 0.002 0.022 3360 Dihedral : 4.540 15.070 2700 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.06 % Allowed : 6.33 % Favored : 92.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.16), residues: 2620 helix: 3.35 (0.18), residues: 700 sheet: 1.84 (0.17), residues: 960 loop : -1.20 (0.16), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 124 TYR 0.007 0.001 TYR P 143 PHE 0.009 0.001 PHE K 55 TRP 0.008 0.001 TRP R 92 HIS 0.003 0.002 HIS Q 68 Details of bonding type rmsd covalent geometry : bond 0.00223 (19280) covalent geometry : angle 0.45058 (26420) hydrogen bonds : bond 0.05287 ( 915) hydrogen bonds : angle 3.38301 ( 3135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 293 time to evaluate : 0.745 Fit side-chains REVERT: B 50 GLN cc_start: 0.8900 (mt0) cc_final: 0.8549 (mt0) REVERT: D 116 SER cc_start: 0.8708 (p) cc_final: 0.8265 (m) REVERT: E 94 ASP cc_start: 0.7768 (m-30) cc_final: 0.7247 (m-30) REVERT: E 101 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7721 (tp30) REVERT: F 56 ASP cc_start: 0.8607 (t0) cc_final: 0.8391 (t70) REVERT: F 59 ASN cc_start: 0.9011 (t0) cc_final: 0.8719 (t0) REVERT: G 59 ASN cc_start: 0.8959 (t0) cc_final: 0.8545 (t0) REVERT: I 25 ILE cc_start: 0.8878 (mt) cc_final: 0.8606 (mm) REVERT: J 56 ASP cc_start: 0.8657 (t70) cc_final: 0.8454 (t0) REVERT: J 94 ASP cc_start: 0.8034 (m-30) cc_final: 0.7703 (t0) REVERT: K 54 ASP cc_start: 0.8583 (t70) cc_final: 0.8381 (t0) REVERT: K 121 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8430 (mt-10) REVERT: M 130 ASP cc_start: 0.8140 (m-30) cc_final: 0.7924 (m-30) REVERT: N 130 ASP cc_start: 0.8503 (m-30) cc_final: 0.8265 (m-30) REVERT: O 69 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8280 (tp30) REVERT: P 59 ASN cc_start: 0.9039 (t0) cc_final: 0.8584 (t0) REVERT: P 77 ASP cc_start: 0.8972 (m-30) cc_final: 0.8741 (m-30) REVERT: Q 50 GLN cc_start: 0.8652 (mt0) cc_final: 0.8421 (mt0) REVERT: Q 59 ASN cc_start: 0.9088 (t0) cc_final: 0.8723 (t0) REVERT: Q 101 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7825 (tt0) REVERT: S 101 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7488 (tp30) REVERT: S 130 ASP cc_start: 0.8173 (m-30) cc_final: 0.7842 (m-30) REVERT: T 121 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8516 (mt-10) outliers start: 23 outliers final: 9 residues processed: 301 average time/residue: 0.4916 time to fit residues: 170.3659 Evaluate side-chains 284 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 273 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain S residue 101 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 8 optimal weight: 0.5980 chunk 42 optimal weight: 0.4980 chunk 246 optimal weight: 6.9990 chunk 225 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 238 optimal weight: 0.8980 chunk 198 optimal weight: 5.9990 chunk 210 optimal weight: 0.8980 chunk 233 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 256 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN F 50 GLN H 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.118916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.101658 restraints weight = 21679.775| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 1.48 r_work: 0.2782 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 19280 Z= 0.104 Angle : 0.442 5.574 26420 Z= 0.245 Chirality : 0.042 0.149 3320 Planarity : 0.002 0.022 3360 Dihedral : 4.442 14.886 2700 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.78 % Allowed : 7.39 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.16), residues: 2620 helix: 3.41 (0.18), residues: 700 sheet: 1.95 (0.17), residues: 960 loop : -1.23 (0.16), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 124 TYR 0.005 0.001 TYR P 143 PHE 0.010 0.001 PHE K 55 TRP 0.009 0.001 TRP R 92 HIS 0.004 0.002 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00223 (19280) covalent geometry : angle 0.44224 (26420) hydrogen bonds : bond 0.05248 ( 915) hydrogen bonds : angle 3.32909 ( 3135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 283 time to evaluate : 0.668 Fit side-chains REVERT: B 50 GLN cc_start: 0.8884 (mt0) cc_final: 0.8477 (mt0) REVERT: C 50 GLN cc_start: 0.8815 (OUTLIER) cc_final: 0.8597 (mt0) REVERT: D 116 SER cc_start: 0.8646 (p) cc_final: 0.8215 (m) REVERT: E 94 ASP cc_start: 0.7835 (m-30) cc_final: 0.7328 (m-30) REVERT: E 101 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7746 (tp30) REVERT: F 56 ASP cc_start: 0.8599 (t0) cc_final: 0.8380 (t70) REVERT: F 59 ASN cc_start: 0.9009 (t0) cc_final: 0.8731 (t0) REVERT: G 59 ASN cc_start: 0.8931 (t0) cc_final: 0.8529 (t0) REVERT: I 25 ILE cc_start: 0.8880 (mt) cc_final: 0.8595 (mm) REVERT: I 50 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8146 (tt0) REVERT: J 56 ASP cc_start: 0.8658 (t70) cc_final: 0.8436 (t70) REVERT: J 88 ASP cc_start: 0.7900 (t0) cc_final: 0.7609 (t0) REVERT: J 94 ASP cc_start: 0.8072 (m-30) cc_final: 0.7792 (t0) REVERT: K 121 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8413 (mt-10) REVERT: L 88 ASP cc_start: 0.7827 (t70) cc_final: 0.7475 (t70) REVERT: M 130 ASP cc_start: 0.8163 (m-30) cc_final: 0.7919 (m-30) REVERT: N 130 ASP cc_start: 0.8511 (m-30) cc_final: 0.8299 (m-30) REVERT: O 69 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8259 (tp30) REVERT: P 59 ASN cc_start: 0.9044 (t0) cc_final: 0.8598 (t0) REVERT: P 77 ASP cc_start: 0.8958 (m-30) cc_final: 0.8724 (m-30) REVERT: Q 50 GLN cc_start: 0.8647 (mt0) cc_final: 0.8415 (mt0) REVERT: Q 59 ASN cc_start: 0.9071 (t0) cc_final: 0.8736 (t0) REVERT: Q 101 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7820 (tt0) REVERT: R 94 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7837 (t0) REVERT: S 101 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7541 (tp30) REVERT: S 130 ASP cc_start: 0.8165 (m-30) cc_final: 0.7799 (m-30) REVERT: T 101 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7843 (mt-10) outliers start: 17 outliers final: 9 residues processed: 287 average time/residue: 0.5129 time to fit residues: 168.4661 Evaluate side-chains 288 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 274 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain I residue 50 GLN Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain R residue 94 ASP Chi-restraints excluded: chain T residue 101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 169 optimal weight: 3.9990 chunk 55 optimal weight: 10.0000 chunk 197 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 82 optimal weight: 0.9990 chunk 115 optimal weight: 0.7980 chunk 232 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 GLN F 50 GLN H 50 GLN J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.115282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.097972 restraints weight = 21793.300| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.47 r_work: 0.2726 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19280 Z= 0.133 Angle : 0.478 6.538 26420 Z= 0.266 Chirality : 0.043 0.146 3320 Planarity : 0.003 0.023 3360 Dihedral : 4.682 16.026 2700 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.24 % Allowed : 7.89 % Favored : 90.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.16), residues: 2620 helix: 3.26 (0.18), residues: 700 sheet: 1.83 (0.17), residues: 960 loop : -1.30 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG G 124 TYR 0.007 0.001 TYR P 143 PHE 0.015 0.001 PHE K 55 TRP 0.012 0.001 TRP R 92 HIS 0.006 0.003 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00300 (19280) covalent geometry : angle 0.47809 (26420) hydrogen bonds : bond 0.06400 ( 915) hydrogen bonds : angle 3.53753 ( 3135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 281 time to evaluate : 0.773 Fit side-chains REVERT: B 50 GLN cc_start: 0.8862 (OUTLIER) cc_final: 0.8539 (mt0) REVERT: C 50 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8602 (mt0) REVERT: D 116 SER cc_start: 0.8743 (p) cc_final: 0.8260 (m) REVERT: E 94 ASP cc_start: 0.7843 (m-30) cc_final: 0.7277 (m-30) REVERT: E 101 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7758 (tp30) REVERT: F 59 ASN cc_start: 0.9023 (t0) cc_final: 0.8773 (t0) REVERT: G 59 ASN cc_start: 0.8962 (t0) cc_final: 0.8569 (t0) REVERT: H 101 GLU cc_start: 0.8232 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: I 25 ILE cc_start: 0.8898 (mt) cc_final: 0.8626 (mm) REVERT: I 101 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: J 56 ASP cc_start: 0.8714 (t70) cc_final: 0.8430 (t70) REVERT: J 88 ASP cc_start: 0.8069 (t0) cc_final: 0.7798 (t0) REVERT: J 94 ASP cc_start: 0.8116 (m-30) cc_final: 0.7839 (t0) REVERT: L 25 ILE cc_start: 0.8560 (mt) cc_final: 0.8249 (tp) REVERT: L 88 ASP cc_start: 0.8026 (t70) cc_final: 0.7634 (t70) REVERT: M 130 ASP cc_start: 0.8228 (m-30) cc_final: 0.7992 (m-30) REVERT: O 25 ILE cc_start: 0.8924 (mt) cc_final: 0.8648 (mm) REVERT: O 69 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8273 (tp30) REVERT: P 59 ASN cc_start: 0.9072 (t0) cc_final: 0.8649 (t0) REVERT: P 77 ASP cc_start: 0.8946 (m-30) cc_final: 0.8716 (m-30) REVERT: Q 50 GLN cc_start: 0.8690 (mt0) cc_final: 0.8462 (mt0) REVERT: Q 59 ASN cc_start: 0.9107 (t0) cc_final: 0.8711 (t160) REVERT: Q 101 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7850 (tt0) REVERT: S 101 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7573 (tp30) REVERT: S 130 ASP cc_start: 0.8299 (m-30) cc_final: 0.7937 (m-30) REVERT: T 101 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7879 (mt-10) outliers start: 27 outliers final: 13 residues processed: 291 average time/residue: 0.5487 time to fit residues: 182.7703 Evaluate side-chains 288 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 268 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 101 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 18 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 247 optimal weight: 0.0570 chunk 90 optimal weight: 5.9990 chunk 168 optimal weight: 0.3980 chunk 253 optimal weight: 5.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN F 50 GLN H 50 GLN J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.110067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.090657 restraints weight = 22455.547| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 1.64 r_work: 0.2726 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2593 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 19280 Z= 0.109 Angle : 0.443 6.807 26420 Z= 0.245 Chirality : 0.042 0.157 3320 Planarity : 0.003 0.022 3360 Dihedral : 4.432 15.103 2700 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.24 % Allowed : 8.85 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.90 (0.16), residues: 2620 helix: 3.46 (0.18), residues: 700 sheet: 1.94 (0.17), residues: 960 loop : -1.32 (0.15), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.007 0.001 TYR P 143 PHE 0.012 0.001 PHE K 55 TRP 0.009 0.001 TRP R 92 HIS 0.004 0.002 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00237 (19280) covalent geometry : angle 0.44304 (26420) hydrogen bonds : bond 0.05413 ( 915) hydrogen bonds : angle 3.31192 ( 3135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 0.773 Fit side-chains REVERT: B 50 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8544 (mt0) REVERT: C 50 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8575 (mt0) REVERT: D 116 SER cc_start: 0.8621 (p) cc_final: 0.8149 (m) REVERT: E 94 ASP cc_start: 0.7794 (m-30) cc_final: 0.7237 (m-30) REVERT: E 101 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7790 (tp30) REVERT: F 59 ASN cc_start: 0.9007 (t0) cc_final: 0.8724 (t0) REVERT: G 22 MET cc_start: 0.8956 (mmp) cc_final: 0.8749 (mmp) REVERT: G 59 ASN cc_start: 0.8943 (t0) cc_final: 0.8560 (t0) REVERT: I 25 ILE cc_start: 0.8863 (mt) cc_final: 0.8578 (mm) REVERT: J 56 ASP cc_start: 0.8580 (t70) cc_final: 0.8288 (t70) REVERT: J 88 ASP cc_start: 0.7973 (t0) cc_final: 0.7712 (t0) REVERT: J 94 ASP cc_start: 0.8037 (m-30) cc_final: 0.7778 (t0) REVERT: K 121 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8388 (mt-10) REVERT: L 25 ILE cc_start: 0.8504 (mt) cc_final: 0.8174 (tp) REVERT: O 25 ILE cc_start: 0.8902 (mt) cc_final: 0.8603 (mm) REVERT: O 69 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8246 (tp30) REVERT: P 59 ASN cc_start: 0.9014 (t0) cc_final: 0.8594 (t0) REVERT: P 77 ASP cc_start: 0.8946 (m-30) cc_final: 0.8715 (m-30) REVERT: Q 50 GLN cc_start: 0.8629 (mt0) cc_final: 0.8391 (mt0) REVERT: Q 59 ASN cc_start: 0.9114 (t0) cc_final: 0.8727 (t160) REVERT: Q 101 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: S 101 GLU cc_start: 0.8028 (OUTLIER) cc_final: 0.7604 (tp30) REVERT: T 101 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7843 (mt-10) outliers start: 27 outliers final: 14 residues processed: 286 average time/residue: 0.5552 time to fit residues: 181.5836 Evaluate side-chains 284 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 265 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain B residue 100 THR Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain Q residue 101 GLU Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 101 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 102 optimal weight: 1.9990 chunk 16 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 32 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 179 optimal weight: 0.0980 chunk 56 optimal weight: 2.9990 chunk 205 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN F 50 GLN H 50 GLN I 50 GLN J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.108991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.091560 restraints weight = 22229.982| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 1.47 r_work: 0.2651 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.1947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 19280 Z= 0.252 Angle : 0.619 8.028 26420 Z= 0.341 Chirality : 0.049 0.180 3320 Planarity : 0.004 0.028 3360 Dihedral : 5.317 20.685 2700 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 1.28 % Allowed : 9.40 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.16), residues: 2620 helix: 2.33 (0.18), residues: 720 sheet: 1.47 (0.17), residues: 960 loop : -1.49 (0.15), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 124 TYR 0.017 0.002 TYR P 143 PHE 0.023 0.003 PHE K 55 TRP 0.018 0.003 TRP R 92 HIS 0.011 0.005 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00621 (19280) covalent geometry : angle 0.61874 (26420) hydrogen bonds : bond 0.08819 ( 915) hydrogen bonds : angle 3.97779 ( 3135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 258 time to evaluate : 0.767 Fit side-chains REVERT: A 40 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8474 (tp) REVERT: A 144 ASN cc_start: 0.8368 (m-40) cc_final: 0.8164 (m110) REVERT: B 50 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8534 (mt0) REVERT: C 50 GLN cc_start: 0.8782 (OUTLIER) cc_final: 0.8405 (mt0) REVERT: D 116 SER cc_start: 0.8906 (p) cc_final: 0.8435 (m) REVERT: E 101 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7947 (mm-30) REVERT: F 59 ASN cc_start: 0.9050 (t0) cc_final: 0.8805 (t0) REVERT: G 25 ILE cc_start: 0.8778 (mt) cc_final: 0.8520 (mm) REVERT: G 59 ASN cc_start: 0.9055 (t0) cc_final: 0.8696 (t0) REVERT: H 40 LEU cc_start: 0.8385 (tt) cc_final: 0.7988 (mt) REVERT: H 101 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7907 (mt-10) REVERT: I 25 ILE cc_start: 0.8888 (mt) cc_final: 0.8647 (mm) REVERT: I 101 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7609 (mm-30) REVERT: O 25 ILE cc_start: 0.8960 (mt) cc_final: 0.8695 (mm) REVERT: P 77 ASP cc_start: 0.8900 (m-30) cc_final: 0.8679 (m-30) REVERT: Q 50 GLN cc_start: 0.8749 (mt0) cc_final: 0.8530 (mt0) REVERT: Q 59 ASN cc_start: 0.9139 (t0) cc_final: 0.8855 (t0) REVERT: S 101 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: T 94 ASP cc_start: 0.8245 (m-30) cc_final: 0.7830 (m-30) REVERT: T 101 GLU cc_start: 0.8117 (OUTLIER) cc_final: 0.7886 (mt-10) outliers start: 28 outliers final: 14 residues processed: 267 average time/residue: 0.5694 time to fit residues: 173.6713 Evaluate side-chains 266 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 245 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain N residue 60 THR Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 101 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 257 optimal weight: 6.9990 chunk 116 optimal weight: 1.9990 chunk 120 optimal weight: 9.9990 chunk 131 optimal weight: 0.9990 chunk 187 optimal weight: 4.9990 chunk 225 optimal weight: 3.9990 chunk 252 optimal weight: 5.9990 chunk 231 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 GLN H 50 GLN J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.103252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.084913 restraints weight = 22862.910| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 1.50 r_work: 0.2645 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.092 19280 Z= 0.239 Angle : 0.609 8.368 26420 Z= 0.335 Chirality : 0.048 0.165 3320 Planarity : 0.004 0.031 3360 Dihedral : 5.409 20.812 2700 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.38 % Allowed : 10.00 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.82 (0.15), residues: 2620 helix: 2.19 (0.18), residues: 720 sheet: 1.25 (0.17), residues: 960 loop : -1.63 (0.14), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 124 TYR 0.018 0.002 TYR P 143 PHE 0.023 0.003 PHE K 55 TRP 0.018 0.003 TRP R 92 HIS 0.010 0.005 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00587 (19280) covalent geometry : angle 0.60928 (26420) hydrogen bonds : bond 0.08614 ( 915) hydrogen bonds : angle 3.97692 ( 3135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 245 time to evaluate : 0.745 Fit side-chains REVERT: A 40 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8468 (tp) REVERT: B 50 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: C 50 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.8485 (mt0) REVERT: C 94 ASP cc_start: 0.8086 (m-30) cc_final: 0.7833 (m-30) REVERT: D 116 SER cc_start: 0.8879 (p) cc_final: 0.8413 (m) REVERT: F 59 ASN cc_start: 0.9064 (t0) cc_final: 0.8827 (t0) REVERT: F 90 LYS cc_start: 0.8828 (mtpp) cc_final: 0.8597 (mtpt) REVERT: G 25 ILE cc_start: 0.8780 (mt) cc_final: 0.8514 (mm) REVERT: G 59 ASN cc_start: 0.9057 (t0) cc_final: 0.8697 (t0) REVERT: H 40 LEU cc_start: 0.8371 (tt) cc_final: 0.7962 (mt) REVERT: H 101 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7967 (mt-10) REVERT: I 25 ILE cc_start: 0.8915 (mt) cc_final: 0.8677 (mm) REVERT: I 101 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7622 (mm-30) REVERT: K 121 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8419 (mt-10) REVERT: M 40 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8093 (tt) REVERT: N 25 ILE cc_start: 0.8977 (mt) cc_final: 0.8568 (mm) REVERT: O 25 ILE cc_start: 0.8961 (mt) cc_final: 0.8692 (mm) REVERT: P 59 ASN cc_start: 0.9222 (t0) cc_final: 0.8844 (t0) REVERT: P 77 ASP cc_start: 0.8869 (m-30) cc_final: 0.8643 (m-30) REVERT: Q 50 GLN cc_start: 0.8763 (mt0) cc_final: 0.8539 (mt0) REVERT: Q 59 ASN cc_start: 0.9134 (t0) cc_final: 0.8859 (t0) REVERT: R 101 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7549 (mm-30) REVERT: S 101 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7621 (tp30) REVERT: T 101 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7831 (mt-10) outliers start: 30 outliers final: 15 residues processed: 254 average time/residue: 0.5895 time to fit residues: 170.2311 Evaluate side-chains 259 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 235 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain C residue 25 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 25 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 100 THR Chi-restraints excluded: chain H residue 101 GLU Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain J residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain M residue 40 LEU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain R residue 40 LEU Chi-restraints excluded: chain R residue 101 GLU Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 101 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 152 optimal weight: 0.7980 chunk 6 optimal weight: 0.9980 chunk 234 optimal weight: 0.0170 chunk 133 optimal weight: 1.9990 chunk 243 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 85 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 138 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 GLN H 50 GLN J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.107265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.087795 restraints weight = 22513.192| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.66 r_work: 0.2724 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19280 Z= 0.127 Angle : 0.480 8.057 26420 Z= 0.265 Chirality : 0.043 0.143 3320 Planarity : 0.003 0.030 3360 Dihedral : 4.760 18.975 2700 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.01 % Allowed : 10.23 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.16), residues: 2620 helix: 2.95 (0.18), residues: 700 sheet: 1.45 (0.17), residues: 960 loop : -1.56 (0.14), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 124 TYR 0.010 0.001 TYR P 143 PHE 0.013 0.001 PHE K 55 TRP 0.011 0.001 TRP R 92 HIS 0.005 0.002 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00288 (19280) covalent geometry : angle 0.47974 (26420) hydrogen bonds : bond 0.06180 ( 915) hydrogen bonds : angle 3.48724 ( 3135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 264 time to evaluate : 0.817 Fit side-chains REVERT: B 50 GLN cc_start: 0.8878 (OUTLIER) cc_final: 0.8485 (mt0) REVERT: C 50 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8616 (mt0) REVERT: D 116 SER cc_start: 0.8765 (p) cc_final: 0.8264 (m) REVERT: E 101 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7868 (tp30) REVERT: F 59 ASN cc_start: 0.9004 (t0) cc_final: 0.8699 (t0) REVERT: G 59 ASN cc_start: 0.8990 (t0) cc_final: 0.8623 (t0) REVERT: I 25 ILE cc_start: 0.8823 (mt) cc_final: 0.8554 (mm) REVERT: J 56 ASP cc_start: 0.8792 (t70) cc_final: 0.8490 (t70) REVERT: J 94 ASP cc_start: 0.8130 (m-30) cc_final: 0.7815 (t0) REVERT: K 121 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8353 (mt-10) REVERT: L 25 ILE cc_start: 0.8504 (mt) cc_final: 0.8165 (tp) REVERT: O 25 ILE cc_start: 0.8896 (mt) cc_final: 0.8610 (mm) REVERT: O 69 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8237 (tp30) REVERT: P 59 ASN cc_start: 0.9068 (t0) cc_final: 0.8688 (t0) REVERT: P 77 ASP cc_start: 0.8961 (m-30) cc_final: 0.8729 (m-30) REVERT: Q 50 GLN cc_start: 0.8711 (mt0) cc_final: 0.8482 (mt0) REVERT: Q 59 ASN cc_start: 0.9094 (t0) cc_final: 0.8791 (t0) REVERT: S 101 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7577 (tp30) REVERT: T 101 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7852 (mt-10) outliers start: 22 outliers final: 10 residues processed: 274 average time/residue: 0.5783 time to fit residues: 180.7065 Evaluate side-chains 266 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 252 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 181 optimal weight: 7.9990 chunk 17 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 220 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 GLN H 50 GLN J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.105192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.085822 restraints weight = 22802.726| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 1.63 r_work: 0.2664 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2529 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19280 Z= 0.158 Angle : 0.523 8.611 26420 Z= 0.287 Chirality : 0.045 0.177 3320 Planarity : 0.003 0.032 3360 Dihedral : 4.906 19.362 2700 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.83 % Allowed : 10.60 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.16), residues: 2620 helix: 2.67 (0.18), residues: 720 sheet: 1.43 (0.17), residues: 960 loop : -1.52 (0.15), residues: 940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 124 TYR 0.013 0.001 TYR P 143 PHE 0.017 0.002 PHE K 55 TRP 0.014 0.002 TRP R 92 HIS 0.007 0.003 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00369 (19280) covalent geometry : angle 0.52311 (26420) hydrogen bonds : bond 0.07010 ( 915) hydrogen bonds : angle 3.63561 ( 3135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5240 Ramachandran restraints generated. 2620 Oldfield, 0 Emsley, 2620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 257 time to evaluate : 0.739 Fit side-chains REVERT: B 50 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8467 (mt0) REVERT: C 50 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8594 (mt0) REVERT: D 116 SER cc_start: 0.8761 (p) cc_final: 0.8258 (m) REVERT: E 101 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7858 (tp30) REVERT: F 59 ASN cc_start: 0.9038 (t0) cc_final: 0.8756 (t0) REVERT: G 59 ASN cc_start: 0.9014 (t0) cc_final: 0.8650 (t0) REVERT: I 25 ILE cc_start: 0.8872 (mt) cc_final: 0.8609 (mm) REVERT: I 101 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7538 (mm-30) REVERT: J 56 ASP cc_start: 0.8823 (t70) cc_final: 0.8516 (t70) REVERT: K 121 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8367 (mt-10) REVERT: L 25 ILE cc_start: 0.8528 (mt) cc_final: 0.8194 (tp) REVERT: N 25 ILE cc_start: 0.8923 (mt) cc_final: 0.8510 (mm) REVERT: O 25 ILE cc_start: 0.8924 (mt) cc_final: 0.8639 (mm) REVERT: P 59 ASN cc_start: 0.9109 (t0) cc_final: 0.8739 (t0) REVERT: P 77 ASP cc_start: 0.8886 (m-30) cc_final: 0.8650 (m-30) REVERT: Q 50 GLN cc_start: 0.8700 (mt0) cc_final: 0.8466 (mt0) REVERT: Q 59 ASN cc_start: 0.9115 (t0) cc_final: 0.8817 (t0) REVERT: S 101 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7562 (tp30) REVERT: T 75 ASP cc_start: 0.8769 (t0) cc_final: 0.8532 (t0) REVERT: T 94 ASP cc_start: 0.7931 (m-30) cc_final: 0.7515 (m-30) REVERT: T 101 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7899 (mt-10) outliers start: 18 outliers final: 12 residues processed: 261 average time/residue: 0.5984 time to fit residues: 177.5683 Evaluate side-chains 274 residues out of total 2180 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 257 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain B residue 50 GLN Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain D residue 25 ILE Chi-restraints excluded: chain F residue 25 ILE Chi-restraints excluded: chain G residue 33 ILE Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain I residue 101 GLU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain L residue 101 GLU Chi-restraints excluded: chain O residue 33 ILE Chi-restraints excluded: chain O residue 56 ASP Chi-restraints excluded: chain P residue 33 ILE Chi-restraints excluded: chain P residue 101 GLU Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain T residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 106 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 chunk 45 optimal weight: 7.9990 chunk 251 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 214 optimal weight: 0.6980 chunk 88 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 chunk 114 optimal weight: 0.0980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 GLN H 50 GLN J 50 GLN L 50 GLN P 50 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.108298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.088959 restraints weight = 22643.577| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 1.64 r_work: 0.2726 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2591 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19280 Z= 0.116 Angle : 0.470 8.476 26420 Z= 0.258 Chirality : 0.043 0.169 3320 Planarity : 0.003 0.031 3360 Dihedral : 4.587 18.198 2700 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 1.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.83 % Allowed : 10.60 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.16), residues: 2620 helix: 3.16 (0.18), residues: 700 sheet: 1.78 (0.17), residues: 940 loop : -1.43 (0.14), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG I 124 TYR 0.009 0.001 TYR P 143 PHE 0.012 0.001 PHE K 55 TRP 0.009 0.001 TRP F 141 HIS 0.005 0.002 HIS E 68 Details of bonding type rmsd covalent geometry : bond 0.00256 (19280) covalent geometry : angle 0.47001 (26420) hydrogen bonds : bond 0.05735 ( 915) hydrogen bonds : angle 3.35817 ( 3135) =============================================================================== Job complete usr+sys time: 5615.97 seconds wall clock time: 96 minutes 50.74 seconds (5810.74 seconds total)